Hi,I'm not a bioinformatic, but I need to perform a sequence alignment between two protein which are not very similar. In this case is better to perform a local alignment, right? I did this kind of aligment with LALIGN tool.What do you think about this tool?

local alignment is best for proteins, which may have the same domain (but others differ), or differ in length in general, or when you look for example for similar residues in the active site. The homology of sequences should be reflected by homology matrix used (compaire e.g. BLOSUM80 vs. BLOSUM62 or PAM250 vs. PAM100).